First, you should use the calculator for the difference between two means. That calculator will present the results you expect.
You used the calculator for k means based on the Analysis of Variance, not a t-test of a simple difference. What if you had 8 means? The 'difference' is captured in the way the ANOVA will work. I attached a detailed explanation in a JMP technical report for you. See Section 2.3, which starts in the middle of page 5.
Second, JMP 17 introduced a whole new class of calculators that we think are superior to the older calculators, which will be deprecated in the future. You might take a look at them here and see what you think. Here is the sample size explorer for two means: